So, yeah, shrinking the weapons down to around 5-8 per Town/Village/City would be a good idea, and then rank them depending on what area is easier to "unlock". Generally it would go: Crossglen, Fallhaven, Villeguard, then Blackwater/Prim. Problem now is that not only weapons, but even Armor/Items, are not any better once you leave Fallhaven. Villguard and Blackwater/Prim don't really add much that you actually want. I think putting better items there would be more important.
Now that the game a general flow, it would be a big deal to do a major overhaul of the weapons/items locations in the next update. I think a 0.7.0 update doing that would be monumental for the game. At least IMHO it would be. I consider that a milestone to reach. While I love the game, I hate playing it with the mentality of "one set of best items only". You should be able to build different characters that want to do different things.
Right now, there is no benefit using any of the AP 6+ weapons. Arguably, unless it's legendary, AP5 is off limits too. AP3 and 4 are just too strong with the Jewel of Fallhaven. Especially Flagstone's Pride (wish I didn't sell mine... learned too late how good JOF is). Right now, Quickstrike/Venemous Dagger or Flagstone's Pride are two acceptable and best weapons to build for. There's no benefit for going the other route. You hit faster, kill faster, and just progress faster with those weapons. With that thought, I came up with Cleave and Stun for the Maces/Hammers/Clubs/Axes, but I feel they should do more as well. Maybe add +EXP per kill? Another advantage that those quicker and lower weapons wouldn't have. I do like that you have a lot of these martial weapons as having Crit % and x2/x3/x4 stats. I think that's good because it lets that one hit matter the most.
If you ask me, I would say that Bonemeal Potions are also the other problem too. Healing in this game is just good. Meat and Bonemeals is so good that once you get to 60+ HP, you don't need to worry. If you get a crit hit, you can heal it off. If the creature multi-strikes and lands lots of blows, you can heal it off (and usually attack some after each bonemeal too). If Meat healed less HP and Bonemeals cost twice, if not three times, as much, then actually worrying about BC% would become more important. I think most players stick with around 60-80% BC, and go 200% AC. Doesn't that seem off-balance? Healing needs to be tweaked in order to address the problem with some of these weapons in my opinion.
This was a long post, but I'm on a PC so I can type more

I think it's all related in a way, and I think it can be a big issue going further into the game.
*I posted my Damage Resistance character in "Equipment - The Good and The Bad" because I liked it. Although it took forever to kill creatures, I rarely needed more than 30 Bonemeals to clear the Gargoyle caves many times over. I had 3 DR and my BC% was near 80%. When I switched to full-AC mode, my BC went down to 50% and 0 DR. I now carry a few hundred Bonemeals - and I need them. If there a better Mace/Hammer/Club weapon that offered a high Min and Max damage, with like 10% crit w/3x multiplier, I'd be rockin' that set of gear. I had no problem getting one attack because I rolled Crit pretty regular and one-hitted guys. If that weapon also had the Cleave/Stun option I mentioned earlier, I'd be doing even better. Not nuts, but a lot better.